Step 1 qt phenotype all nan

[mdelliot]

Hi, I'm trying to run a small test sample for a quantitative trait through step 1 and I cannot get any Output other than the one listed here. Any ideas of what is going wrong? Thank you

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          |      REGENIE v3.1.3.gz      |
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Copyright (c) 2020-2022 Joelle Mbatchou, Andrey Ziyatdinov and Jonathan Marchini. Distributed under the MIT License. Compiled with Boost Iostream library. Using Intel MKL with Eigen.

Log of output saved in file : /Regenie/Step1New/MinMAF1pct/QT/regenieRes.log

WARNING: only variants which satisfy both extract/exclude options will be kept. Options in effect: --step 1 \ --bed /Regenie/allQCBAFilter/allQCBAFilter \ --covarFile /Regenie/CovPheno/covariates.txt \ --phenoFile /Regenie/CovPheno/phenotypesQT.txt \ --qt \ --lowmem \ --apply-rint \ --covarColList U1,U2,U3,U4,U5,U6,sex \ --extract /Regenie/allQCBAFilter/snps.pruned.QT.snplist \ --exclude /Regenie/allQCBAFilter/QT.exclude \ --bsize 100 \ --loocv \ --lowmem-prefix /Regenie/Step1New/MinMAF1pct/QT/ \ --out /Regenie/Step1New/MinMAF1pct/QT/regenieRes

Fitting null model

• bim : [/Regenie/allQCBAFilter/allQCBAFilter.bim] n_snps = 112312 -keeping variants specified by --extract -removing variants specified by --exclude -number of variants remaining in the analysis = 35900
• fam : [/Regenie/allQCBAFilter/allQCBAFilter.fam] n_samples = 166
• bed : [/Regenie/allQCBAFilter/allQCBAFilter.bed]
• phenotypes : [/Regenie/CovPheno/phenotypesQT.txt] n_pheno = 1 -dropping observations with missing values at any of the phenotypes -number of phenotyped individuals with no missing data = 121
• covariates : [Regenie/CovPheno/covariates.txt] n_cov = 7 -number of individuals with covariate data = 166
• number of individuals used in analysis = 121 -applying RINT to all phenotypes
• number of observations for each trait:
  • 'C3': 121 observations -residualizing and scaling phenotypes...done (0ms)

• threads : [47]

• block size : [100]

• blocks : [373] for 35900 variants

• CV folds : [121]

• ridge data_l0 : [5 : 0.01 0.25 0.5 0.75 0.99 ]
• ridge data_l1 : [5 : 0.01 0.25 0.5 0.75 0.99 ]
• approximate memory usage : 960MB
• writing level 0 predictions to disk -temporary files will have prefix [/Regenie/Step1New/MinMAF1pct/QT/_l0_Y] -approximate disk space needed : 3MB
• setting memory...done

With the output of:

Level 1 ridge... -on phenotype 1 (C3)...done (86ms)

Output

phenotype 1 (C3) : 0.01 : Rsq = -nan, MSE = -nan<- min value 0.25 : Rsq = -nan, MSE = -nan 0.5 : Rsq = -nan, MSE = -nan 0.75 : Rsq = -nan, MSE = -nan 0.99 : Rsq = -nan, MSE = -nan

• making predictions...writing LOCO predictions...done (60ms)

and the pred.list file is all -nan

[joellembatchou]

Hi,

Have you checked the distribution of the phenotype for the 121 samples analyzed? Note that we recommend running Step 1 on a fairly large set of variants (eg 500K) to get good genome-wide coverage (here you only have 36K).